Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
H3K4me3 MLL-AF4_AF4-MLL ChIPSeq
cell type
human ESC
genotype/variation
MLL-AF4 and AF4-MLL expression
chip antibody
H3K4me3 (ab8580)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde crosslinked cell extracts were sonicated to 200-500 bp sized particles at 0.5-min intervals with Bioruptor (Diagenode) and the chromatin fraction was divided in three parts and incubated overnight with antibody Libraries were prepared using the kit: NEBNext Ultra DNA Library Prep kit for Illumina (Ref.:#7370) following the commercial protocol. Libraries QC: Bioanalyzer and quantification by qPCR using the kit: KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
7539141
Reads aligned (%)
83.5
Duplicates removed (%)
8.4
Number of peaks
10319 (qval < 1E-05)

hg19

Number of total reads
7539141
Reads aligned (%)
81.8
Duplicates removed (%)
11.1
Number of peaks
10341 (qval < 1E-05)

Base call quality data from DBCLS SRA